The detection of gene mutations in patients with congenitally missing teeth is not very complicated; however, proving causality is often quite difficult. Here, we report the detection of a substitution mutation, A42P, within the prodomain of bone morphogenetic protein 4 (BMP4) in a small family with tooth agenesis and describe a functional alteration that may be responsible for the tooth phenotype. As BMP4 is essential for the development of teeth and also for many other organs, it would be of considerable interest to find a BMP4 mutation that is associated only with tooth agenesis. Our in vitro investigations revealed that the A42P mutation neither affected processing and secretion of BMP4 nor altered functional properties, such as the induction of alkaline phosphatase or signaling through Smad1/5/8 phosphorylation by the mature BMP4 ligand. However, immunofluorescence staining revealed that the prodomains of BMP4 which harbor the A42P substitution form fibrillar structures around transfected cells in culture and that this fibrillar network is significantly decreased when mutant prodomains are expressed. Our finding suggests that in vivo, BMP4 prodomain behavior might also be altered by the mutation and could influence storage or transport of mature BMP4 in the extracellular matrix of the developing tooth.